NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P04916 UniProt NPD GO	RETBP_RAT	Plasma retinol-binding protein precursor (PRBP) (RBP)	0.12	-	mit	0	Secreted protein				201
P81286 UniProt NPD GO	PLMN_SHEEP	Plasminogen (EC 3.4.21.7) (Fragment)	0.12	-	cyt	0	Secreted protein				343
P22777 UniProt NPD GO	PAI1_MOUSE	Plasminogen activator inhibitor 1 precursor (PAI-1) (Endothelial plasminogen activator inhibitor) (P ...	0.12	-	mit	0	Secreted protein				402
P48531 UniProt NPD GO	PTA2_XENLA	Pleiotrophic factor-alpha-2 precursor (PTF-alpha-2)	0.12	-	nuc	0	Secreted protein (By similarity)				142
O08581 UniProt NPD GO	KCNK1_MOUSE	Potassium channel subfamily K member 1 (Inward rectifying potassium channel protein TWIK-1)	0.12	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	endosome [IDA]			336
Q9JL58 UniProt NPD GO	KCNK9_CAVPO	Potassium channel subfamily K member 9 (Acid-sensitive potassium channel protein TASK-3) (TWIK-relat ...	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				365
P45660 UniProt NPD GO	KAX17_LEIQH	Potassium channel toxin alpha-KTx 1.7 (Toxin 15-1) (Lqh 15-1)	0.12	-	nuc	0	Secreted protein				36
P80719 UniProt NPD GO	KAX62_SCOMA	Potassium channel toxin alpha-KTx 6.2 (Maurotoxin) (MTX)	0.12	-	nuc	0	Secreted protein			1WT7	34
Q9UKI3 UniProt NPD GO	VPRE3_HUMAN	Pre-B lymphocyte protein 3 precursor (VpreB3 protein) (N27C7-2)	0.12	-	exc	0		endoplasmic reticulum [NAS]	605017		123
Q90ZE4 UniProt NPD GO	PSN2_BRARE	Presenilin-2 (EC 3.4.23.-) (PS2) (Zf-PS2) (Pre2)	0.12	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				441
Q5XJY4 UniProt NPD GO	PARL_MOUSE	Presenilins-associated rhomboid-like protein, mitochondrial precursor (EC 3.4.21.105) (Mitochondrial ...	0.12	-	mit	6	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity). Mitochondr ...				377
Q66H88 UniProt NPD GO	PPAC2_RAT	Presqualene diphosphate phosphatase (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 domain-contai ...	0.12	-	end	3	Membrane; multi-pass membrane protein (Potential)				293
Q6F4C6 UniProt NPD GO	PMN14_PINFU	Prismalin-14 precursor	0.12	-	exc	0					121
P56942 UniProt NPD GO	MCH_MOUSE	Pro-MCH precursor [Contains: Neuropeptide-glycine-glutamic acid (NGE) (Neuropeptide G-E); Neuropepti ...	0.12	-	exc	0	Secreted protein (By similarity)	extracellular region [IC]			166
Q3SYR3 UniProt NPD GO	ABEC2_BOVIN	Probable C->U-editing enzyme APOBEC-2 (EC 3.5.4.-)	0.12	-	cyt	0					224
P46091 UniProt NPD GO	GPR1_HUMAN	Probable G-protein coupled receptor 1	0.12	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600239		355
O97664 UniProt NPD GO	GPR1_MACMU	Probable G-protein coupled receptor 1	0.12	-	end	7 *	Membrane; multi-pass membrane protein				355
Q7TQN9 UniProt NPD GO	GP142_MOUSE	Probable G-protein coupled receptor 142	0.12	-	end	7	Membrane; multi-pass membrane protein				365
Q7Z7M1 UniProt NPD GO	GP144_HUMAN	Probable G-protein coupled receptor 144 (G-protein coupled receptor PGR24)	0.12	-	end	5	Membrane; multi-pass membrane protein	integral to membrane [TAS]			963
Q9NS67 UniProt NPD GO	GPR27_HUMAN	Probable G-protein coupled receptor 27 (Super conserved receptor expressed in brain 1)	0.12	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)		605187		375
Q49SQ1 UniProt NPD GO	GPR33_HUMAN	Probable G-protein coupled receptor 33	0.12	-	end	7 *	Membrane; multi-pass membrane protein				333
Q09502 UniProt NPD GO	YQH2_CAEEL	Probable G-protein coupled receptor C43C3.2	0.12	-	end	7	Membrane; multi-pass membrane protein (Potential)				498
Q9LGE6 UniProt NPD GO	LSM4_ORYSA	Probable U6 snRNA-associated Sm-like protein LSm4	0.12	+	cyt	0	Nucleus (Potential)				147
Q9ZRU9 UniProt NPD GO	LSM4_FAGSY	Probable U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein 2)	0.12	-	cyt	0	Nucleus (Potential)				148
O82039 UniProt NPD GO	SPY_PETHY	Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY (EC 2.4.1.-) (PhSP ...	0.12	-	cyt	0	Nucleus (By similarity)				932
Q9URZ0 UniProt NPD GO	AGAL_SCHPO	Probable alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrola ...	0.12	-	exc	1 *		external side of plasma membrane [TAS]			436
Q8NDH3 UniProt NPD GO	PEPL1_HUMAN	Probable aminopeptidase NPEPL1 (EC 3.4.11.-) (Aminopeptidase-like 1)	0.12	+	cyt	0					523
Q22492 UniProt NPD GO	HEXA_CAEEL	Probable beta-hexosaminidase A precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acety ...	0.12	-	cyt	0	Lysosome (Potential)				555
P0C197 UniProt NPD GO	CLCNX_USTMA	Probable chloride channel protein UM03490-D	0.12	-	end	11	Membrane; multi-pass membrane protein (Potential)				1131
Q9FHI7 UniProt NPD GO	DRL35_ARATH	Probable disease resistance protein At5g45490	0.12	-	cyt	0					354
O14238 UniProt NPD GO	OST2_SCHPO	Probable dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost2 (EC 2.4.1.119) ...	0.12	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				122
O04487 UniProt NPD GO	EF1G1_ARATH	Probable elongation factor 1-gamma 1 (EF-1-gamma 1) (eEF-1B gamma 1)	0.12	-	cyt	0					414
Q9C641 UniProt NPD GO	EFGM_ARATH	Probable elongation factor G, mitochondrial precursor (mEF-G)	0.12	-	nuc	0	Mitochondrion				754
P38695 UniProt NPD GO	HXT5_YEAST	Probable glucose transporter HXT5	0.12	-	end	11	Membrane; multi-pass membrane protein				592
Q9MAQ0 UniProt NPD GO	SSG1_ARATH	Probable granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch ...	0.12	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound (By similarity)				610
Q9GP38 UniProt NPD GO	MANA_ECHMU	Probable mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomut ...	0.12	-	cyt	0	Cytoplasm (By similarity)				433
P40504 UniProt NPD GO	KTR7_YEAST	Probable mannosyltransferase KTR7 (EC 2.4.1.131)	0.12	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				517
Q9N361 UniProt NPD GO	RT25_CAEEL	Probable mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25)	0.12	-	cyt	0	Mitochondrion (By similarity)				170
P33759 UniProt NPD GO	RT05_YEAST	Probable mitochondrial 40S ribosomal protein S5	0.12	-	mit	0	Mitochondrion (Potential)	mitochondrial small ribosomal subunit [IDA]			307
Q9VGA2 UniProt NPD GO	TI17C_DROME	Probable mitochondrial import inner membrane translocase subunit Tim17 3	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	integral to membrane [ISS] mitochondrial inner membrane presequence tr... [ISS]			222
Q12013 UniProt NPD GO	AKR2_YEAST	Probable palmitoyltransferase AKR2 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR2)	0.12	-	end	7	Membrane; multi-pass membrane protein (Probable)				749
Q9D6H5 UniProt NPD GO	ZDHC4_MOUSE	Probable palmitoyltransferase ZDHHC4 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 4) (DH ...	0.12	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				343
O62515 UniProt NPD GO	PAHX_CAEEL	Probable phytanoyl-CoA dioxygenase (EC 1.14.11.18) (Phytanoyl-CoA alpha-hydroxylase) (PhyH) (Phytani ...	0.12	-	cyt	0					312
Q67ZM7 UniProt NPD GO	PHYK2_ARATH	Probable phytol kinase 2, chloroplast precursor (EC 2.7.-.-)	0.12	-	end	7	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				307
Q7XPL3 UniProt NPD GO	HAK15_ORYSA	Probable potassium transporter 15 (OsHAK15)	0.12	-	end	13	Membrane; multi-pass membrane protein (By similarity)				867
Q10143 UniProt NPD GO	PFD3_SCHPO	Probable prefoldin subunit 3	0.12	-	mit	0					169
Q7Z996 UniProt NPD GO	POP8_SCHPO	Probable ribonucleases P protein subunit pop8 (EC 3.1.26.5)	0.12	-	cyt	0	Nucleus (Potential)				108
Q5R5C9 UniProt NPD GO	SCPDH_PONPY	Probable saccharopine dehydrogenase (EC 1.5.1.9)	0.12	-	nuc	1					429
Q61CQ8 UniProt NPD GO	SPCS1_CAEBR	Probable signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit ...	0.12	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				113
Q9LW86 UniProt NPD GO	SUT34_ARATH	Probable sulfate transporter 3.4	0.12	-	end	11	Membrane; multi-pass membrane protein (Potential)				653

You are viewing entries 61651 to 61700 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.